I would have preferred AtGames provide a solution but it wasn't meant to be.
Looking at that site I'm not actually sure what the solution is for Flashback 9 HDMI owners.
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2600daptor will not work with the FB9 for paddles. My point is that the FB9 is just running an emulator called Stella. You can run this emulator on many other devices that can be used with original paddles (unaltered) using the 2600daptor.
I will also point out that even when running the most recent version of Stella on a modern gaming PC, the paddle latency is (despite the best efforts of the community) still quite laggy. The way the paddle position is read depends on some variables that are simply much faster with original hardware on a CRT TV. I've tested this extensively with Kaboom - you just can't get the same scores in Stella as you can on the real thing. In that way it is like the Mike Tyson's Punch Out of VCS games.
My point is that even if you get paddles to work on your computer or on the FB9, the experience is still a far distance from the original thing. If you don't have original hardware, you'd be better off just running an emulator on your computer occasionally to get your Kaboom fix. Hacking up paddles to interface with an inferior experience takes you even farther away from what you ultimately are after.